We report the complication of corneal endothelial staining with trypan blue that limited the surgical view during cataract extraction in a 10-month-old boy. The boy had presented with a pigmentary retinopathy, microphthalmia, and a dense, white, unilateral congenital cataract. He was suspected of having, and was later diagnosed with, congenital rubella syndrome. We hypothesize that the corneal staining may have resulted from virally induced corneal endothelial damage. To our knowledge, this is the first reported case of trypan blue adversely affecting congenital cataract surgery.